#massspec

ASMS

@asms.org

2 days ago

Planning your time in San Diego? #ASMS2026 Short Courses take place in person at the Annual Conference and offer a great opportunity to build your skills and learn directly from experts in #MassSpec. #MassSpecCommunity #TeamMassSpec

https://bit.ly/4tQOE3z

Simon Stael

@simonstael.bsky.social

3 days ago

#PlantScience, #PlantSci, #PlantBiology, #PlantSciJobs,
@plantpostdocs.bsky.social , #ComputationalProteomics, #Proteomics, #Bioinformatics, #MassSpec, #StructuralProteomics, #CompMS, @plantscience.bsky.social, @proteocure.bsky.social, @proteomicsnews.bsky.social

Mann Lab

@mannlab.bsky.social

5 days ago

3/3 Mass Spectrometry-Based Proteomics Postdoc — work at the cutting edge of MS-based biology in one of the world's leading proteomics groups! Apply → postdocprogram.mpg.de/node/43386
#MassSpec #PostDoc #Parkinson

@jasms.bsky.social

1 week ago

Which JASMS papers had a moment this month? 👀
Explore the most-read articles and see what the mass spectrometry community has been diving into: bit.ly/4pOfir4
#MassSpec #MassSpecCommunity

ASMS

@asms.org

1 week ago

Which @jasms.bsky.social papers had a moment this month? 👀
Explore the most-read articles and see what the mass spectrometry community has been diving into: bit.ly/4pOfir4
#MassSpec #MassSpecCommunity

Florian Huber

@me-datapoint.bsky.social

1 week ago

New MS2DeepScore release (2.9.0) 🚀
--> github.com/matchms/ms2d...

The main change is the ability to use count and log-count rdkit fingerprints, as well as unfolded fingerprints for training.

#opensource #massspec #Python

ASMS

@asms.org

1 week ago

Welcome to Incoming #ASMS Archivist-Historian Mariam ElNaggar! After ten incredible years of service Jane Gale will pass the torch at the end of the year.

Learn about our History Projects:
https://www.asms.org/about/history

#MassSpec #TeamMassSpec #FeMS

Matrix Science

@matrixscience.bsky.social

1 week ago

Mascot Newsletter logo.

Mascot Newsletter, March 2026:

Search BLIB spectral libraries with Mascot.

PET hydrolase expressed in fruit flies.

UK office has moved.

www.matrixscience.com/nl/202603/ne...

#proteomics #massspec

SNP2Prot

@snp2prot.bsky.social

1 week ago

A Native Nepenthesin Reactor for Improved Proteolytic Digestion of Intrinsically Disordered Proteins in Proteomics Workflows A workflow is presented for the extraction and purification of native nepenthesin (NEP-NAT) from Nepenthes species, followed by the enzyme's immobilization on POROS-AL chromatographic material. The N...

Latest publication from SNP2Prot colleagues C. Wall and A. Sinz reveals that the Nepenthesin protease, isolated from 𝘕𝘦𝘱𝘦𝘯𝘵𝘩𝘦𝘴 sp., carries superior proteolytic activity towards IDPs.

Kudos to the team 🎉

doi.org/10.1002/cbic...

#MassSpec #Protease #IDPs
#Proteomics

@sinzandrea.bsky.social

Spectrometrics Limited

@spectrometrix.bsky.social

1 week ago

Is your lab short on electrical outlets. Spectrometrics has a range of add-ons that typically let you pull the plug on at least two outlets per #MassSpec system.

Matrix Science

@matrixscience.bsky.social

1 week ago

matrixscience.com is being overwhelmed by millions of HTTP requests from distributed botnets, essentially a distributed denial of service (DDoS) attack. We are forced to mitigate it by restrict access to certain pages of dynamic content.

www.matrixscience.com/whats_new/mi...

#proteomics #massspec

Shimadzu UK

@shimadzuuk.bsky.social

1 week ago

Shimadzu at London Biological Mass Spectrometry Discussion Group

Today we're pleased to be supporting @bio-mass-spec-ldn.bsky.social at Burlington House.
If you're here too, come and say hi to our LCMS specialists, Ollie Sligsby-Wolfe & Emma Poole!

#analysis #biosciences #massspec #massspectrometry #lcms #lbmsdg
#SciSky #AcademicSky #ChemSky #EduSky #Edchat 🧪

Matrix Science

@matrixscience.bsky.social

2 weeks ago

Bar chart comparison of standard acqusition method compared to Thunder-DDA-PASEF.

Thunder-DDA-PASEF is an acquisition strategy for capturing more human leukocyte antigen (HLA) class I peptide ligands on Bruker timsTOF instruments. This month's blog shows how you can process Thunder-DDA-PASEF data with Mascot Distiller.

www.matrixscience.com/blog/process...

#proteomics #massspec

Will Fondrie

@willfondrie.com

2 weeks ago

I 100% agree with this take.

Plug: If you are working with #proteomics and/or #massspec data, check out our shortcourse at #ASMS2026 to get a jump start on many of these methods! (Course 04 here: www.asms.org/conferences/...)

BIOE Paper

@bioescript.bsky.social

2 weeks ago

MSInet: A Self-Supervised CNN Framework Integrating Global and Local Context for Robust Mass Spectrometry Imaging Segmentation Mass spectrometry imaging (MSI) enables label-free molecular mapping in tissues but presents challenges for spatial segmentation due to high dimensionality, nonlinear spectral variation, and tissue he...

What's your biggest segmentation challenge?

🧠 Complex brain anatomy (many subregions)
🔬 Tumor heterogeneity (cancer vs. necrosis vs. healthy)
📊 Choosing cluster numbers (k=?)
🌀 Fragmented results

pubs.acs.org/doi/10.1021/...

#MassSpec #SpatialOmics #DeepLearning #Metabolomics

(4/4)

BioMassSpec

@realbiomassspec.bsky.social

2 weeks ago

Multiomics Analysis across the Life Cycle Identifies Zn2Cys6_61 as a Target for Enhancing Triterpenoid Production in Ganoderma lucidum Ganoderic acids (GAs) are high-value lanostane-type triterpenoids derived from Ganoderma lucidum (G. lucidum) with broad applications in functional foods and nutraceuticals, yet their low natural abundance limits industrial production. In this study, an integrated life-cycle multiomics analysis combining metabolomics, transcriptomics, and proteomics was conducted across six developmental stages in four G. lucidum strains to elucidate regulatory mechanisms governing GA biosynthesis. Weighted gene coexpression network analysis identified candidate cytochrome P450 enzymes and transcription factors associated with GA accumulation. A Zn2Cys6-type transcription factor, Zn2Cys6_61, was identified as a central regulator and functionally validated through overexpression and RNA interference. Genetic manipulation of Zn2Cys6_61 expression significantly altered GA levels, with overexpression markedly enhancing GA accumulation. Further analysis demonstrated that Zn2Cys6_61 directly binds to and activates the promoter of squalene synthase, a key enzyme in triterpenoid backbone biosynthesis. Together, these findings identify Zn2Cys6_61 as an effective engineering target and provide a transcription factor-based strategy for improving GA production in medicinal mushrooms.

Multiomics Analysis across the Life Cycle Identifies Zn2Cys6_61 as a Target for Enhancing Triterpenoid Production in Ganoderma lucidum #JAFC #MassSpec pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

2 weeks ago

Metabolomics-Guided Integration of a “Push–Pull-Restrain” Strategy for Enhanced LNnT Production in Saccharomyces cerevisiae Lacto-N-neotetraose (LNnT) is a prominent neutral human milk oligosaccharide (HMO) with limited availability. Here, Saccharomyces cerevisiae (GRAS strain, Generally Recognized as Safe) was metabolically engineered to enhance LNnT production. Metabolomics analysis revealed that competition from chitin synthesis and insufficient metabolic driving force for heterologous glycosyltransferases in yeast constituted major metabolic bottlenecks. To overcome these limitations, a “push–pull-restraint” strategy was applied, integrating glycosyltransferase screening, protein tag fusion evaluation, targeted chitin disruption of chitin biosynthetic genes, and balanced modulation of UDP-Gal/UDP-GlcNAc supply. These interventions increased extracellular LNnT titer in shake-flask cultures from 14.65 mg/L to 1.66 g/L, with total LNnT reaching 2.01 g/L. Further scale-up in a 5 L bioreactor under fed-batch conditions resulted in a total LNnT titer of 4.70 g/L. These results demonstrate the potential for the production of LNnT by S. cerevisiae and open up an innovative framework for the effective synthesis of LNnT.

Metabolomics-Guided Integration of a “Push–Pull-Restrain” Strategy for Enhanced LNnT Production in Saccharomyces cerevisiae #JAFC #MassSpec pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

2 weeks ago

Systematic Evaluation of the Impact of Storage Time on Label-Free Proteomics of Colorectal Adenocarcinoma Formalin-Fixed Paraffin-Embedded Tissues Mass spectrometry (MS)-based proteomics has empowered comprehensive protein profiling of biological specimens. However, formalin-fixed paraffin-embedded (FFPE) tissues─critical resources for clinical biomarker discovery-remain underexplored in the setting of long-term storage (>15 years). Herein, we systematically evaluated the impact of storage time on proteomic analyses of 80 colorectal adenocarcinoma (CRC) FFPE samples, which were stratified by two key variables: storage time (>15 years vs <1 year) and tissue type (tumor vs adjacent normal tissue). We adopted a standardized protein extraction strategy, and subsequent proteomic profiling was performed via data-dependent acquisition and data-independent acquisition MS workflows. Our results demonstrated that FFPE tissue storage time impacts protein extraction efficiency, peptide yields, PTM identification, and protein quantification. The impacts were more pronounced on the peptide level. However, the biological enrichments (Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis) from the global proteome profile and from differentially expressed proteins in CRC tissues were independent of archival time. Five clinically relevant biomarkers of CRC were further validated via immunohistochemistry. Collectively, our findings confirm that FFPE tissues retain stability for proteomic analyses even following >15 years of storage, thereby providing critical insights for leveraging archival FFPE biobanks to advance clinical proteomics and archival pathology research.

Systematic Evaluation of the Impact of Storage Time on Label-Free Proteomics of Colorectal Adenocarcinoma Formalin-Fixed Paraffin-Embedded Tissues #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

2 weeks ago

Graph Machine Learning Can Estimate Drug Concentrations in Whole Blood from Forensic Screening Results LC-HRMS is widely used in forensic toxicology for broad-scope screening. When a newly emerging or rarely encountered compound is tentatively identified, toxicologists must decide whether it may be relevant to a case and, if so, quantify it. However, acquiring reference material for quantification is costly and time-consuming. A rapid semiquantitative estimation method would help prioritize only compounds above the toxic threshold. This study presents a machine-learning (ML) framework that estimates drug concentrations in whole blood using molecular structure information and LC-HRMS signals. Using a data set of 191 drugs spiked into whole blood at multiple concentration levels, we trained and evaluated several ML models. Standard models, including Random Forests, achieved moderate performance. In contrast, a recently reported Graph Neural Network (GNN) leveraging atomic features and global molecular properties consistently produced the highest accuracy. Under cross-validation, the GNN predicted signal-to-concentration ratios for 79% of all molecules, corresponding to concentration estimates between 50% and 200% of the true value. Toxicological thresholds often span multiple orders of magnitude, making this precision acceptable. The GNN model was additionally evaluated on an external benchmark data set of ionization efficiencies (logIE), where it outperformed the current state of the art. Overall, the results demonstrate the feasibility of using graph-based ML to estimate drug concentrations in whole blood without reference material. This is a practical ML tool that can support decision-making in toxicological evaluation, particularly for newly emerging or rarely encountered drugs. The GNN model is open source, and the data set used for training and testing the models are publicly available.

Graph Machine Learning Can Estimate Drug Concentrations in Whole Blood from Forensic Screening Results #AC #MassSpec pubs.acs.org/doi/10.1021/...

@jasms.bsky.social

2 weeks ago

Development of Low-Flow High-Resolution Desorption Electrospray Ionization Mass Spectrometry Imaging Desorption electrospray ionization mass spectrometry (DESI-MS) imaging is a well-established technique for molecular analysis of biological samples, although its spatial resolution has been limited when compared to other MS imaging techniques. Here, we...

Catch up on trending research! Read more: Development of Low-Flow High-Resolution Desorption Electrospray Ionization Mass Spectrometry Imaging https://bit.ly/3N2pVsm

#ASMS #JASMS #TeamMassSpec #MassSpec

ASMS

@asms.org

2 weeks ago

Development of Low-Flow High-Resolution Desorption Electrospray Ionization Mass Spectrometry Imaging Desorption electrospray ionization mass spectrometry (DESI-MS) imaging is a well-established technique for molecular analysis of biological samples, although its spatial resolution has been limited when compared to other MS imaging techniques. Here, we...

Catch up on trending research! Read more: Development of Low-Flow High-Resolution Desorption Electrospray Ionization Mass Spectrometry Imaging https://bit.ly/3N2pVsm

#ASMS #JASMS #TeamMassSpec #MassSpec

Dr A.Cooper

@aniacooper.bsky.social

3 weeks ago

Gradually changing peaks in a chromatogram

An underestimated issue in LC-MS: gradual changes in peak shape.
A bit more tailing here, more fronting there... and suddenly your quantitation is drifting.
When you see peak shape change, what's the first thing you check?

#MassSpec #troubleshooting #SciSky #AcademicSky #ChemSky #EduSky #Edchat

Florian Huber

@me-datapoint.bsky.social

3 weeks ago

MS2DeepScore 2.0 is finally published 🚀 --> www.nature.com/articles/s41...

This was a great journey with Niek de Jonge and a great team of collaborators! See more on LinkedIn: www.linkedin.com/posts/f-hube...

#massspec #cheminformatics #ML #opensource #openscience #python

Proteomes MDPI

@proteomesmdpi.bsky.social

3 weeks ago

This article is now available in Proteomes: Scout-Triggered Multiple Reaction Monitoring Enables Robust Quantification of Host Cell Proteins Across Bioprocess Matrices 🧬🖥️🧪🧫🥼

www.mdpi.com/2227-7382/14...

#proteomes #proteomics #proteoform #HCP #MassSpec

BioMassSpec

@realbiomassspec.bsky.social

3 weeks ago

Metabolic disparities of potentially toxic components derived from Psoraleae Fructus and Euodiae Fructus within the Sishen wan influenced by varying compatibilities and physiological conditions in an ... Sishen wan (SSW) is utilized in the treatment of irritable bowel syndrome (IBS). This study aimed to compare gut microbiota-mediated metabolic profile…

Metabolic disparities of potentially toxic components derived from Psoraleae Fructus and Euodiae Fructus within the Sishen wan influenced by varying compatibilities and physiological conditions in an in vitro gut microbiota model #JPBA #MassSpec www.sciencedirect.com/science/arti...

BioMassSpec

@realbiomassspec.bsky.social

3 weeks ago

Glycoinformatic profiling of label-free intact heparan sulfate oligosaccharides Heparan sulfates (HS) are a group of heterogenous linear, sulfated polysaccharides that play a role in in health and many diseases including cancer, cardiovascular, and kidney diseases. The structural...

Glycoinformatic profiling of label-free intact heparan sulfate oligosaccharides #MCP #MassSpec www.mcponline.org/article/S153...

BioMassSpec

@realbiomassspec.bsky.social

3 weeks ago

Supramolecular Solvent Extraction for Doping Control Analysis of Prohibited Substances in Horse Urine This paper describes the first application of supramolecular solvent extraction for doping control analysis of prohibited substances in horse urine.

Supramolecular Solvent Extraction for Doping Control Analysis of Prohibited Substances in Horse Urine #DTA #MassSpec analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...

BioMassSpec

@realbiomassspec.bsky.social

3 weeks ago

Spatial localization and pharmacodynamic assessment of intracrine androgen metabolism in CRPC xenograft tumor tissues upon active vitamin D treatment - Analytical and Bioanalytical Chemistry Castrate-resistant prostate cancer (CRPC) progression is driven by intracrine androgen synthesis despite low circulating androgens. This study investigates the effects of active vitamin D (1,25-(OH)₂-...

Spatial localization and pharmacodynamic assessment of intracrine androgen metabolism in CRPC xenograft tumor tissues upon active vitamin D treatment #ABC #MassSpec link.springer.com/article/10.1...

BioMassSpec

@realbiomassspec.bsky.social

3 weeks ago

A new multi-residue method for PFAS analysis in wastewater for environmental and public health risk assessment - Analytical and Bioanalytical Chemistry This work focuses on the detection and quantification of per-/polyfluorinated alkyl substances (PFAS) in influent wastewater, using wastewater-based epidemiology via a new multi-residue ultra performa...

A new multi-residue method for PFAS analysis in wastewater for environmental and public health risk assessment #ABC #MassSpec link.springer.com/article/10.1...

BioMassSpec

@realbiomassspec.bsky.social

3 weeks ago

Proteomics and Lipidomics Analysis Reveal That Membrane Remodeling and Extracellular Matrix Alterations Are Crucial for Cisplatin Resistance in Triple-Negative Breast Cancer Cisplatin is a widely used chemotherapeutic agent for triple-negative breast cancer (TNBC), but resistance remains a major challenge. Understanding the molecular alterations driving this resistance is essential for identifying therapeutic targets. In this study, we employed an integrated proteomics and lipidomics approach to elucidate key pathways associated with cisplatin resistance. Employing high-resolution mass spectrometry, we conducted a comparative analysis between cisplatin-resistant (cisR) and cisplatin-sensitive (cisS) TNBC cell lines to discover resistance-associated alterations in protein and lipid expression. Proteomic analysis revealed overexpression of extracellular matrix (ECM) remodeling proteins, COL6A1, COL6A2, COL6A3, and VTN, that support epithelial-mesenchymal transition (EMT) and chemoresistance. Membrane-associated proteins such as TIMP2, MMP14, and APP were also elevated, indicating enhanced invasive and pro-survival signaling. Lipidomic alterations, including upregulation of FABP3, FABP4, LPL, and downregulation of PLA2G4A, indicated increased lipid uptake, metabolic rewiring, and membrane restructuring. Notably, elevated long-chain phosphatidylcholines and decreased sphingomyelins suggested increased membrane rigidity and reduced cisplatin permeability. Additionally, dysregulation of CDK activity through CCND2, CCND3, and CCNB2 overexpression indicated accelerated cell cycle progression and evasion of DNA damage checkpoints. Together, this integrative analysis highlights ECM remodeling, cytoskeletal dynamics, and lipid metabolism as major contributors to cisplatin resistance and identifies potential therapeutic markers for TNBC.

Proteomics and Lipidomics Analysis Reveal That Membrane Remodeling and Extracellular Matrix Alterations Are Crucial for Cisplatin Resistance in Triple-Negative Breast Cancer #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...